Starting phenix.real_space_refine on Fri Jul 3 00:54:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zqs_14874/07_2026/7zqs_14874.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zqs_14874/07_2026/7zqs_14874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zqs_14874/07_2026/7zqs_14874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zqs_14874/07_2026/7zqs_14874.map" model { file = "/net/cci-nas-00/data/ceres_data/7zqs_14874/07_2026/7zqs_14874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zqs_14874/07_2026/7zqs_14874.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zqs_14874/07_2026/7zqs_14874.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zqs_14874/07_2026/7zqs_14874.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 60 5.49 5 Mg 4 5.21 5 S 28 5.16 5 C 7068 2.51 5 N 1936 2.21 5 O 2258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11354 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 634 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "B" Number of atoms: 4971 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 639, 4964 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 613} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 7, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 75 Conformer: "B" Number of residues, atoms: 639, 4964 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 613} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 7, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 75 bond proxies already assigned to first conformer: 5075 Chain: "C" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 634 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 4971 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 639, 4964 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 613} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 7, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 75 Conformer: "B" Number of residues, atoms: 639, 4964 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 613} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 7, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 75 bond proxies already assigned to first conformer: 5075 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.90, per 1000 atoms: 0.34 Number of scatterers: 11354 At special positions: 0 Unit cell: (129.514, 107.505, 93.9615, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 60 15.00 Mg 4 11.99 O 2258 8.00 N 1936 7.00 C 7068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 801 " - " ASN B 251 " " NAG D 801 " - " ASN D 251 " " NAG E 1 " - " ASN B 317 " " NAG F 1 " - " ASN B 727 " " NAG G 1 " - " ASN D 317 " " NAG H 1 " - " ASN D 727 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 868.4 milliseconds 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 12 sheets defined 45.1% alpha, 16.9% beta 8 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'B' and resid 123 through 137 removed outlier: 3.716A pdb=" N SER B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 Processing helix chain 'B' and resid 159 through 176 Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 263 through 274 removed outlier: 3.609A pdb=" N LEU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 419 through 439 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 460 through 470 Processing helix chain 'B' and resid 470 through 475 Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 527 through 532 removed outlier: 3.665A pdb=" N VAL B 532 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 removed outlier: 4.173A pdb=" N PHE B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 582 through 603 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 613 through 626 removed outlier: 3.741A pdb=" N GLN B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 639 through 663 Processing helix chain 'B' and resid 667 through 684 removed outlier: 3.765A pdb=" N VAL B 681 " --> pdb=" O ARG B 677 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU B 682 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR B 683 " --> pdb=" O MET B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 722 Processing helix chain 'B' and resid 727 through 751 removed outlier: 3.677A pdb=" N GLY B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.630A pdb=" N ILE B 756 " --> pdb=" O VAL B 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 137 removed outlier: 3.716A pdb=" N SER D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 148 Processing helix chain 'D' and resid 159 through 176 Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 263 through 274 removed outlier: 3.609A pdb=" N LEU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 419 through 439 Processing helix chain 'D' and resid 455 through 459 Processing helix chain 'D' and resid 460 through 470 Processing helix chain 'D' and resid 470 through 475 Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 527 through 532 removed outlier: 3.664A pdb=" N VAL D 532 " --> pdb=" O ALA D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 547 removed outlier: 4.174A pdb=" N PHE D 544 " --> pdb=" O ALA D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 580 Processing helix chain 'D' and resid 582 through 603 Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing helix chain 'D' and resid 613 through 626 removed outlier: 3.741A pdb=" N GLN D 617 " --> pdb=" O ARG D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 635 Processing helix chain 'D' and resid 639 through 663 Processing helix chain 'D' and resid 667 through 684 removed outlier: 3.764A pdb=" N VAL D 681 " --> pdb=" O ARG D 677 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU D 682 " --> pdb=" O VAL D 678 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR D 683 " --> pdb=" O MET D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 722 Processing helix chain 'D' and resid 727 through 751 removed outlier: 3.676A pdb=" N GLY D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 756 removed outlier: 3.630A pdb=" N ILE D 756 " --> pdb=" O VAL D 753 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 180 through 182 removed outlier: 7.150A pdb=" N TYR B 402 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ILE B 482 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 404 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE B 555 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 180 through 182 removed outlier: 7.150A pdb=" N TYR B 402 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ILE B 482 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 404 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE B 555 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 185 through 192 Processing sheet with id=AA4, first strand: chain 'B' and resid 209 through 214 removed outlier: 5.615A pdb=" N LEU B 212 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE B 202 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA6, first strand: chain 'B' and resid 232 through 234 Processing sheet with id=AA7, first strand: chain 'D' and resid 180 through 182 removed outlier: 7.150A pdb=" N TYR D 402 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE D 482 " --> pdb=" O TYR D 402 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL D 404 " --> pdb=" O ILE D 482 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE D 555 " --> pdb=" O ASN D 483 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 180 through 182 removed outlier: 7.150A pdb=" N TYR D 402 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N ILE D 482 " --> pdb=" O TYR D 402 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL D 404 " --> pdb=" O ILE D 482 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE D 555 " --> pdb=" O ASN D 483 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 185 through 192 Processing sheet with id=AB1, first strand: chain 'D' and resid 209 through 214 removed outlier: 5.613A pdb=" N LEU D 212 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE D 202 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 220 through 221 Processing sheet with id=AB3, first strand: chain 'D' and resid 232 through 234 518 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2618 1.33 - 1.45: 2783 1.45 - 1.57: 6181 1.57 - 1.69: 118 1.69 - 1.80: 48 Bond restraints: 11748 Sorted by residual: bond pdb=" C3' DG C 31 " pdb=" C2' DG C 31 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DG A 14 " pdb=" C2' DG A 14 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG A 31 " pdb=" C2' DG A 31 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DG C 14 " pdb=" C2' DG C 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.74e+00 bond pdb=" C1' DC C 27 " pdb=" N1 DC C 27 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 8.95e+00 ... (remaining 11743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 15447 1.31 - 2.62: 668 2.62 - 3.93: 86 3.93 - 5.24: 25 5.24 - 6.55: 6 Bond angle restraints: 16232 Sorted by residual: angle pdb=" N3 DT C 21 " pdb=" C4 DT C 21 " pdb=" O4 DT C 21 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT C 22 " pdb=" C4 DT C 22 " pdb=" O4 DT C 22 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N VAL B 250 " pdb=" CA VAL B 250 " pdb=" C VAL B 250 " ideal model delta sigma weight residual 106.21 110.71 -4.50 1.07e+00 8.73e-01 1.77e+01 angle pdb=" N3 DT A 21 " pdb=" C4 DT A 21 " pdb=" O4 DT A 21 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N VAL D 250 " pdb=" CA VAL D 250 " pdb=" C VAL D 250 " ideal model delta sigma weight residual 106.21 110.68 -4.47 1.07e+00 8.73e-01 1.74e+01 ... (remaining 16227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 6294 34.25 - 68.51: 322 68.51 - 102.76: 16 102.76 - 137.01: 0 137.01 - 171.26: 4 Dihedral angle restraints: 6636 sinusoidal: 2918 harmonic: 3718 Sorted by residual: dihedral pdb=" CA PHE B 313 " pdb=" C PHE B 313 " pdb=" N PRO B 314 " pdb=" CA PRO B 314 " ideal model delta harmonic sigma weight residual -180.00 -158.90 -21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA PHE D 313 " pdb=" C PHE D 313 " pdb=" N PRO D 314 " pdb=" CA PRO D 314 " ideal model delta harmonic sigma weight residual 180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" C4' DG A 31 " pdb=" C3' DG A 31 " pdb=" O3' DG A 31 " pdb=" P DT A 32 " ideal model delta sinusoidal sigma weight residual 220.00 48.74 171.26 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1503 0.054 - 0.109: 293 0.109 - 0.163: 36 0.163 - 0.218: 6 0.218 - 0.272: 2 Chirality restraints: 1840 Sorted by residual: chirality pdb=" CB ILE D 262 " pdb=" CA ILE D 262 " pdb=" CG1 ILE D 262 " pdb=" CG2 ILE D 262 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE B 262 " pdb=" CA ILE B 262 " pdb=" CG1 ILE B 262 " pdb=" CG2 ILE B 262 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 727 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.67e-01 ... (remaining 1837 not shown) Planarity restraints: 1848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 261 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C LYS D 261 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS D 261 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE D 262 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 261 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C LYS B 261 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS B 261 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE B 262 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 740 " -0.016 2.00e-02 2.50e+03 1.02e-02 2.60e+00 pdb=" CG TRP D 740 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP D 740 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP D 740 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 740 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 740 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 740 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 740 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 740 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 740 " -0.003 2.00e-02 2.50e+03 ... (remaining 1845 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2608 2.79 - 3.31: 10660 3.31 - 3.84: 20892 3.84 - 4.37: 25782 4.37 - 4.90: 41451 Nonbonded interactions: 101393 Sorted by model distance: nonbonded pdb=" OP2 DG A 34 " pdb="MG MG A 101 " model vdw 2.257 2.170 nonbonded pdb=" OP2 DG C 34 " pdb="MG MG C 101 " model vdw 2.259 2.170 nonbonded pdb=" O LEU B 387 " pdb=" NH2 ARG B 409 " model vdw 2.267 3.120 nonbonded pdb=" O LEU D 387 " pdb=" NH2 ARG D 409 " model vdw 2.268 3.120 nonbonded pdb=" OP2 DA C 35 " pdb="MG MG C 101 " model vdw 2.269 2.170 ... (remaining 101388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 120 through 639 or resid 641 through 801)) selection = (chain 'D' and (resid 120 through 639 or resid 641 through 801)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.950 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11758 Z= 0.296 Angle : 0.616 6.547 16262 Z= 0.426 Chirality : 0.045 0.272 1840 Planarity : 0.003 0.031 1842 Dihedral : 18.335 171.262 4244 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.24), residues: 1278 helix: 1.49 (0.22), residues: 544 sheet: 0.94 (0.34), residues: 202 loop : 0.33 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 623 TYR 0.013 0.001 TYR D 309 PHE 0.019 0.002 PHE D 313 TRP 0.027 0.002 TRP D 740 HIS 0.004 0.001 HIS B 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.30 (11748) covalent geometry : angle 0.61267 / 0.43 (16232) hydrogen bonds : bond 0.15010 / 15.95 ( 498) hydrogen bonds : angle 5.85480 / 6.22 ( 1464) link_BETA1-4 : bond 0.00265 / 0.20 ( 4) link_BETA1-4 : angle 2.02082 / 3.92 ( 12) link_NAG-ASN : bond 0.00157 / 0.13 ( 6) link_NAG-ASN : angle 1.33549 / 2.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.362 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.7002 time to fit residues: 21.3078 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.070989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.053290 restraints weight = 43085.001| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.68 r_work: 0.2735 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11758 Z= 0.147 Angle : 0.572 7.960 16262 Z= 0.314 Chirality : 0.046 0.338 1840 Planarity : 0.004 0.030 1842 Dihedral : 21.004 175.780 2000 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.19 % Allowed : 1.71 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.24), residues: 1278 helix: 1.71 (0.23), residues: 540 sheet: 1.07 (0.36), residues: 194 loop : 0.45 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 155 TYR 0.011 0.001 TYR D 309 PHE 0.019 0.002 PHE D 313 TRP 0.024 0.002 TRP D 740 HIS 0.003 0.001 HIS B 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (11748) covalent geometry : angle 0.57000 / 0.31 (16232) hydrogen bonds : bond 0.05518 / 5.64 ( 498) hydrogen bonds : angle 4.32543 / 4.91 ( 1464) link_BETA1-4 : bond 0.00207 / 0.15 ( 4) link_BETA1-4 : angle 1.35452 / 2.60 ( 12) link_NAG-ASN : bond 0.00191 / 0.20 ( 6) link_NAG-ASN : angle 1.31706 / 2.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.389 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 22 average time/residue: 0.6064 time to fit residues: 14.8432 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 76 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.071237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.053697 restraints weight = 43169.577| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.67 r_work: 0.2745 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11758 Z= 0.140 Angle : 0.521 6.473 16262 Z= 0.290 Chirality : 0.044 0.326 1840 Planarity : 0.003 0.030 1842 Dihedral : 20.837 174.133 2000 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.24), residues: 1278 helix: 1.80 (0.23), residues: 540 sheet: 1.13 (0.35), residues: 202 loop : 0.47 (0.30), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 155 TYR 0.010 0.001 TYR D 309 PHE 0.018 0.001 PHE D 313 TRP 0.023 0.002 TRP B 740 HIS 0.003 0.001 HIS D 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (11748) covalent geometry : angle 0.51899 / 0.29 (16232) hydrogen bonds : bond 0.04968 / 5.22 ( 498) hydrogen bonds : angle 4.05882 / 4.68 ( 1464) link_BETA1-4 : bond 0.00295 / 0.20 ( 4) link_BETA1-4 : angle 1.20832 / 2.32 ( 12) link_NAG-ASN : bond 0.00181 / 0.17 ( 6) link_NAG-ASN : angle 1.27737 / 2.14 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.401 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6397 time to fit residues: 15.6204 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.071647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.054130 restraints weight = 42633.784| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.66 r_work: 0.2757 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11758 Z= 0.124 Angle : 0.514 6.908 16262 Z= 0.286 Chirality : 0.043 0.320 1840 Planarity : 0.003 0.032 1842 Dihedral : 20.831 174.297 2000 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.24), residues: 1278 helix: 1.92 (0.23), residues: 540 sheet: 1.12 (0.35), residues: 202 loop : 0.52 (0.30), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 668 TYR 0.011 0.001 TYR B 309 PHE 0.017 0.001 PHE B 313 TRP 0.023 0.002 TRP D 740 HIS 0.002 0.001 HIS D 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (11748) covalent geometry : angle 0.51134 / 0.29 (16232) hydrogen bonds : bond 0.04581 / 4.81 ( 498) hydrogen bonds : angle 3.95325 / 4.57 ( 1464) link_BETA1-4 : bond 0.00269 / 0.18 ( 4) link_BETA1-4 : angle 1.22653 / 2.37 ( 12) link_NAG-ASN : bond 0.00162 / 0.16 ( 6) link_NAG-ASN : angle 1.28102 / 2.21 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.478 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6187 time to fit residues: 15.1464 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 125 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.071299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.053737 restraints weight = 42634.272| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.66 r_work: 0.2749 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11758 Z= 0.146 Angle : 0.511 5.975 16262 Z= 0.285 Chirality : 0.044 0.313 1840 Planarity : 0.003 0.031 1842 Dihedral : 20.788 173.661 2000 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.24), residues: 1278 helix: 1.90 (0.22), residues: 540 sheet: 1.09 (0.37), residues: 186 loop : 0.56 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 668 TYR 0.010 0.001 TYR D 470 PHE 0.017 0.001 PHE D 313 TRP 0.023 0.002 TRP D 740 HIS 0.003 0.001 HIS B 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (11748) covalent geometry : angle 0.50825 / 0.28 (16232) hydrogen bonds : bond 0.04379 / 4.71 ( 498) hydrogen bonds : angle 3.88771 / 4.54 ( 1464) link_BETA1-4 : bond 0.00235 / 0.16 ( 4) link_BETA1-4 : angle 1.26877 / 2.45 ( 12) link_NAG-ASN : bond 0.00146 / 0.13 ( 6) link_NAG-ASN : angle 1.28602 / 2.14 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.390 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6091 time to fit residues: 14.8106 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.071271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.053379 restraints weight = 53864.219| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.94 r_work: 0.2730 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11758 Z= 0.153 Angle : 0.509 6.024 16262 Z= 0.283 Chirality : 0.043 0.313 1840 Planarity : 0.003 0.031 1842 Dihedral : 20.790 173.533 2000 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.24), residues: 1278 helix: 1.90 (0.22), residues: 540 sheet: 1.11 (0.37), residues: 186 loop : 0.56 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 155 TYR 0.010 0.001 TYR B 470 PHE 0.018 0.001 PHE B 313 TRP 0.022 0.002 TRP D 740 HIS 0.002 0.001 HIS B 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (11748) covalent geometry : angle 0.50609 / 0.28 (16232) hydrogen bonds : bond 0.04382 / 4.72 ( 498) hydrogen bonds : angle 3.87269 / 4.52 ( 1464) link_BETA1-4 : bond 0.00234 / 0.16 ( 4) link_BETA1-4 : angle 1.26964 / 2.47 ( 12) link_NAG-ASN : bond 0.00159 / 0.12 ( 6) link_NAG-ASN : angle 1.26898 / 2.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.388 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6499 time to fit residues: 15.8144 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 90 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 29 optimal weight: 7.9990 chunk 32 optimal weight: 0.4980 chunk 44 optimal weight: 0.0670 chunk 115 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.073005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.055531 restraints weight = 42726.558| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.65 r_work: 0.2795 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11758 Z= 0.106 Angle : 0.481 5.933 16262 Z= 0.270 Chirality : 0.042 0.307 1840 Planarity : 0.003 0.031 1842 Dihedral : 20.710 172.435 2000 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.25), residues: 1278 helix: 2.01 (0.23), residues: 542 sheet: 1.23 (0.37), residues: 186 loop : 0.66 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 668 TYR 0.011 0.001 TYR D 309 PHE 0.017 0.001 PHE B 313 TRP 0.021 0.002 TRP D 740 HIS 0.001 0.000 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.11 (11748) covalent geometry : angle 0.47875 / 0.27 (16232) hydrogen bonds : bond 0.04037 / 4.30 ( 498) hydrogen bonds : angle 3.74341 / 4.34 ( 1464) link_BETA1-4 : bond 0.00404 / 0.27 ( 4) link_BETA1-4 : angle 1.18707 / 2.34 ( 12) link_NAG-ASN : bond 0.00245 / 0.23 ( 6) link_NAG-ASN : angle 1.22247 / 2.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.360 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.5834 time to fit residues: 15.4359 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 3 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 92 optimal weight: 0.0980 chunk 121 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.072381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.054355 restraints weight = 60802.989| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.09 r_work: 0.2751 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11758 Z= 0.122 Angle : 0.482 5.554 16262 Z= 0.270 Chirality : 0.042 0.302 1840 Planarity : 0.003 0.032 1842 Dihedral : 20.708 172.268 2000 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.19 % Allowed : 4.19 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.24), residues: 1278 helix: 2.00 (0.22), residues: 542 sheet: 1.23 (0.37), residues: 186 loop : 0.68 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 668 TYR 0.010 0.001 TYR D 309 PHE 0.017 0.001 PHE B 313 TRP 0.022 0.002 TRP D 740 HIS 0.002 0.001 HIS D 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (11748) covalent geometry : angle 0.47942 / 0.27 (16232) hydrogen bonds : bond 0.04016 / 4.35 ( 498) hydrogen bonds : angle 3.72515 / 4.36 ( 1464) link_BETA1-4 : bond 0.00257 / 0.17 ( 4) link_BETA1-4 : angle 1.23179 / 2.35 ( 12) link_NAG-ASN : bond 0.00152 / 0.13 ( 6) link_NAG-ASN : angle 1.20926 / 2.02 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.370 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 25 average time/residue: 0.5905 time to fit residues: 16.4698 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 60 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.072857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.055090 restraints weight = 53411.715| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.93 r_work: 0.2761 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11758 Z= 0.126 Angle : 0.482 5.644 16262 Z= 0.270 Chirality : 0.042 0.302 1840 Planarity : 0.003 0.032 1842 Dihedral : 20.709 172.079 2000 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.24), residues: 1278 helix: 2.02 (0.22), residues: 542 sheet: 1.23 (0.37), residues: 186 loop : 0.69 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 623 TYR 0.010 0.001 TYR D 309 PHE 0.017 0.001 PHE B 313 TRP 0.022 0.002 TRP D 740 HIS 0.002 0.001 HIS D 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (11748) covalent geometry : angle 0.47964 / 0.27 (16232) hydrogen bonds : bond 0.03990 / 4.34 ( 498) hydrogen bonds : angle 3.69548 / 4.33 ( 1464) link_BETA1-4 : bond 0.00265 / 0.18 ( 4) link_BETA1-4 : angle 1.22590 / 2.36 ( 12) link_NAG-ASN : bond 0.00150 / 0.13 ( 6) link_NAG-ASN : angle 1.18845 / 2.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.417 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.6326 time to fit residues: 15.4566 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 11 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 86 optimal weight: 0.0570 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 25 optimal weight: 0.4980 chunk 34 optimal weight: 0.0670 chunk 108 optimal weight: 0.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.073753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.056253 restraints weight = 42942.958| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.67 r_work: 0.2803 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 11758 Z= 0.102 Angle : 0.469 5.564 16262 Z= 0.264 Chirality : 0.041 0.299 1840 Planarity : 0.003 0.033 1842 Dihedral : 20.663 171.604 2000 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.25), residues: 1278 helix: 2.07 (0.23), residues: 542 sheet: 1.26 (0.37), residues: 186 loop : 0.73 (0.30), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 623 TYR 0.010 0.001 TYR D 309 PHE 0.016 0.001 PHE B 313 TRP 0.023 0.002 TRP D 740 HIS 0.001 0.000 HIS D 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.10 (11748) covalent geometry : angle 0.46633 / 0.26 (16232) hydrogen bonds : bond 0.03825 / 4.13 ( 498) hydrogen bonds : angle 3.64832 / 4.26 ( 1464) link_BETA1-4 : bond 0.00342 / 0.24 ( 4) link_BETA1-4 : angle 1.19139 / 2.28 ( 12) link_NAG-ASN : bond 0.00214 / 0.19 ( 6) link_NAG-ASN : angle 1.14272 / 1.93 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.337 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.6012 time to fit residues: 16.6059 Evaluate side-chains 22 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 28 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.071109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.053146 restraints weight = 51861.337| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.91 r_work: 0.2727 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11758 Z= 0.189 Angle : 0.520 5.792 16262 Z= 0.288 Chirality : 0.044 0.304 1840 Planarity : 0.003 0.038 1842 Dihedral : 20.742 171.982 2000 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.24), residues: 1278 helix: 1.93 (0.22), residues: 542 sheet: 1.21 (0.37), residues: 186 loop : 0.68 (0.29), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 155 TYR 0.013 0.001 TYR B 470 PHE 0.017 0.002 PHE D 731 TRP 0.022 0.002 TRP D 740 HIS 0.004 0.001 HIS D 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (11748) covalent geometry : angle 0.51721 / 0.29 (16232) hydrogen bonds : bond 0.04213 / 4.67 ( 498) hydrogen bonds : angle 3.76399 / 4.46 ( 1464) link_BETA1-4 : bond 0.00157 / 0.09 ( 4) link_BETA1-4 : angle 1.33835 / 2.53 ( 12) link_NAG-ASN : bond 0.00098 / 0.05 ( 6) link_NAG-ASN : angle 1.24042 / 2.08 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2994.34 seconds wall clock time: 52 minutes 6.61 seconds (3126.61 seconds total)